Probabilistic knowledge representation using the principle of maximum entropy and Gröbner basis theory

An often used methodology for reasoning with probabilistic conditional knowledge bases is provided by the principle of maximum entropy (so-called MaxEnt principle) that realises an idea of least amount of assumed information and thus of being as unbiased as possible. In this paper we exploit the fact that MaxEnt distributions can be computed by solving nonlinear equation systems that reflect the conditional logical structure of these distributions. We apply the theory of Gröbner bases that is well known from computational algebra to the polynomial system which is associated with a MaxEnt distribution, in order to obtain results for reasoning with maximum entropy. We develop a three-phase compilation scheme extracting from a knowledge base consisting of probabilistic conditionals the information which is crucial for MaxEnt reasoning and transforming it to a Gröbner basis. Based on this transformation, a necessary condition for knowledge bases to be consistent is derived. Furthermore, approaches to answering MaxEnt queries are presented by demonstrating how inferring the MaxEnt probability of a single conditional from a given knowledge base is possible. Finally, we discuss computational methods to establish general MaxEnt inference rules.     

Fault detection and isolation in robotic manipulators via neural networks: A comparison among three architectures for residual analysis

In this article we discuss artificial neural networks‐based fault detection and isolation (FDI) applications for robotic manipulators. The artificial neural networks (ANNs) are used for both residual generation and residual analysis. A multilayer perceptron (MLP) is employed to reproduce the dynamics of the robotic manipulator. Its outputs are compared with actual position and velocity measurements, generating the so‐called residual vector. The residuals, when properly analyzed, provides an indication of the status of the robot (normal or faulty operation). Three ANNs architectures are employed in the residual analysis. The first is a radial basis function network (RBFN) which uses the residuals of position and velocity to perform fault identification. The second is again an RBFN, except that it uses only the velocity residuals. The third is an MLP which also performs fault identification utilizing only the velocity residuals. The MLP is trained with the classical back‐propagation algorithm and the RBFN is trained with a Kohonen self‐organizing map (KSOM). We validate the concepts discussed in a thorough simulation study of a Puma 560 and with experimental results with a 3‐joint planar manipulator. © 2001 John Wiley & Sons, Inc.     

Evaluating ASP and Commercial Solvers on the CSPLib

This paper deals with four solvers for combinatorial problems: the commercial state-of-the-art solver ILOG oplstudio, and the research answer set programming (ASP) systems dlv, smodels and cmodels. The first goal of this research is to evaluate the relative performance of such systems when used in a purely declarative way, using a reproducible and extensible experimental methodology. In particular, we consider a third-party problem library, i.e., the CSPLib, and uniform rules for modelling and instance selection. The second goal is to analyze the marginal effects of popular reformulation techniques on the various solving technologies. In particular, we consider structural symmetry breaking, the adoption of global constraints, and the addition of auxiliary predicates. Finally, we evaluate, on a subset of the problems, the impact of numbers and arithmetic constraints on the different solving technologies. Results show that there is not a single solver winning on all problems, and that reformulation is almost always beneficial: symmetry-breaking may be a good choice, but its complexity has to be carefully chosen, by taking into account also the particular solver used. Global constraints often, but not always, help opl, and the addition of auxiliary predicates is usually worth, especially when dealing with ASP solvers. Moreover, interesting synergies among the various modelling techniques exist.     

Atomic force microscopy of protein films and crystals

A customized atomic force microscopy (AFM) instrument optimized for imaging protein crystals in solution is described. The device was tested on crystals and Langmuir-Blodgett (LB) films of two proteins with quite different molecular weights. This approach enables the periodicity and morphology of crystals to be studied in their mother liquid, thereby preserving the native periodic protein crystal structure, which is typically destroyed by drying. Moreover, the instrument appears to distinguish protein crystals from salt crystals, which under the optical microscope are frequently quite similar, the difference between them often being revealed only during x-ray analysis. AFM estimates of the packing, order, and morphology of the given single proteins appear quite similar in the LB thin film and in the crystals, which means that routine crystal measurements can be performed at high resolution. The AFM consists of a custom-built measuring head and a homemade flexible SPM controller which can drive the head for contact, noncontact and spectroscopy modes, thus providing the user with a high degree of customization for crystal measurement.     

An efficient deconvolution algorithm for estimating oxygen consumption during muscle activities

The reconstruction of an unknown input function from noisy measurements in a biological system is an ill-posed inverse problem. Any computational algorithm for its solution must use some kind of regularization technique to neutralize the disastrous effects of amplified noise components on the computed solution. In this paper, following a hierarchical Bayesian statistical inversion approach, we seek estimates for the input function and regularization parameter (hyperparameter) that maximize the posterior probability density function. We solve the maximization problem simultaneously for all unknowns, hyperparameter included, by a suitably chosen quasi-Newton method. The optimization approach is compared to the sampling-based Bayesian approach. We demonstrate the efficiency and robustness of the deconvolution algorithm by applying it to reconstructing the time courses of mitochondrial oxygen consumption during muscle state transitions (e.g., from resting state to contraction and recovery), from the simulated noisy output of oxygen concentration dynamics on the muscle surface. The model of oxygen transport and metabolism in skeletal muscle assumes an in vitro cylindrical structure of the muscle in which the oxygen from the surrounding oxygenated solution diffuses into the muscle and is then consumed by the muscle mitochondria. The algorithm can be applied to other deconvolution problems by suitably replacing the forward model of the system.     

The multimod application framework: a rapid application development tool for computer aided medicine

This paper describes a new application framework (OpenMAF) for rapid development of multimodal applications in computer-aided medicine. MAF applications are multimodal in data, in representation, and in interaction. The framework supports almost any type of biomedical data, including DICOM datasets, motion-capture recordings, or data from computer simulations (e.g. finite element modeling). The interactive visualization approach (multimodal display) helps the user interpret complex datasets, providing multiple representations of the same data. In addition, the framework allows multimodal interaction by supporting the simultaneous use of different input-output devices like 3D trackers, stereoscopic displays, haptics hardware and speech recognition/synthesis systems. The Framework has been designed to run smoothly even on limited power computers, but it can take advantage of all hardware capabilities. The Framework is based on a collection of portable libraries and it can be compiled on any platform that supports OpenGL, including Windows, MacOS X and any flavor of Unix/linux.     

Stepwise dissection and visualization of the catalytic mechanism of haloalkane dehalogenase LinB using molecular dynamics simulations and computer graphics

The different steps of the dehalogenation reaction carried out by LinB on three different substrates have been characterized using a combination of quantum mechanical calculations and molecular dynamics simulations. This has allowed us to obtain information in atomic detail about each step of the reaction mechanism, that is, substrate entrance and achievement of the near-attack conformation, transition state stabilization within the active site, halide stabilization, water molecule activation and subsequent hydrolytic attack on the ester intermediate with formation of alcohol, and finally product release. Importantly, no bias or external forces were applied during the whole procedure so that both intermediates and products were completely free to sample configuration space in order to adapt to the plasticity of the active site and/or search for an exit. Differences in substrate reactivity were found to be correlated with the ease of adopting the near-attack conformation and two different exit pathways were found for product release that do not interfere with substrate entrance. Additional support for the different entry and exit pathways was independently obtained from an examination of the enzyme's normal modes.     

Subacute proteome changes following traumatic injury of the developing brain: Implications for a dysregulation of neuronal migration and neurite arborization

Traumatic brain injury (TBI) is a major cause of morbidity and mortality among children and adolescents. To gain insight into developmental events influenced by TBI, we analyzed subacute mouse brain proteome changes in a percussion head trauma model at P7 ipsi- and contralateral to the site of injury. The comparison of brain proteomes of trauma mice and controls revealed reproducible changes in the intensity of 28 proteins (30 protein spots) in response to trauma. The changes detected suggest that TBI leads to apoptosis, inflammation, and oxidative stress. These changes were consistent with our results of histological and biochemical evaluation of the brains which revealed widespread apoptotic neurodegeneration, microglia activation, and increased levels of protein carbonyls. Furthermore, we detected changes in proteins involved in neuronal migration as well as axonal and dendritic growth and guidance, suggesting interference of trauma with these developmental events.     

A web-based e-learning system for increasing study efficiency by stimulating learner’s motivation

Due to the opportunities provided by the Internet, more and more people are taking advantage of distance learning courses and during the last few years enormous research efforts have been dedicated to the development of distance learning systems. So far, many e-learning systems are proposed and used practically. However, in these systems the e-learning completion rate is about 30%. One of the reasons is the low study desire when the learner studies the learning materials. In this research, we propose an interactive Web-based e-learning system. The purpose of our system is to increase the e-learning completion rate by stimulating learner’s motivation. The proposed system has three subsystems: the learning subsystem, learner support subsystem, and teacher support subsystem. The learning subsystem improves the learner’s study desire. The learner support subsystem supports the learner during the study, and the teacher support subsystem supports the teacher to get the learner’s study state. To evaluate the proposed system, we developed several experiments and surveys. By using new features such as: display of learner’s study history, change of interface color, encourage function, ranking function, self-determination of the study materials, and grouping of learners, the proposed system can increase the learning efficiency.

Ambient occlusion and edge cueing to enhance real time molecular visualization

The paper presents a set of combined techniques to enhance the real-time visualization of simple or complex molecules (up to order of 106 atoms) space fill mode. The proposed approach includes an innovative technique for efficient computation and storage of ambient occlusion terms, a small set of GPU accelerated procedural impostors for space-fill and ball-and-stick rendering, and novel edge-cueing techniques. As a result, the user's understanding of the three-dimensional structure under inspection is strongly increased (even for still images), while the rendering still occurs in real time.